Treatment of pancreatic and related cancers with 5-acyl-6,7-dihydrothieno[3,2-c}pyridines

ABSTRACT

Methods for inhibiting the growth of pancreatic cancer cells or other cancer cells driven by Sonic hedgehog are disclosed. The method involves exposing the cells to 5-acyl-6,7-dihydrothieno[3,2-c]pyridines of formula (I)

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Patent ApplicationNo. 61/614,954, filed Mar. 23, 2012, which is hereby incorporated hereinin by reference.

STATEMENT AS TO RIGHTS UNDER FEDERALLY-SPONSORED RESEARCH

This invention was made with Government support under Contracts Nos.GM57966 and CA158474, awarded by the National Institutes of Health.Accordingly, the U.S. Government has certain rights in this invention.

FIELD OF THE INVENTION

The invention relates to 5-acyl-6,7-dihydrothieno[3,2-c]pyridines thatare useful for treating pancreatic cancer and other types of cancersthat are associated with aberrant expression of Hedgehog proteins.

BACKGROUND OF THE INVENTION

Pancreatic cancer is the fourth most common cause of cancer death in theworld, and it has a poor prognosis. For all stages combined, the 1- and5-year relative survival rates are 25% and 6%, respectively; the mediansurvival for locally advanced and for metastatic disease, whichcollectively represent over 80% of individuals, is about 10 and 6 monthsrespectively. It is estimated that in the United States in 2012 therewill be 43,920 new cases and 37,390 deaths.

Hedgehog (Hh) and Sonic Hedgehog (Shh) are signaling proteins thatmediate growth and patterning during embryonic development. Theseproteins act as morphogens to form long and short range signalinggradients. Hh is expressed in flies, while vertebrates express 3 familymembers: Sonic, Indian and Desert, of which Shh is the best studied. Shhregulates limb development, cell proliferation and differentiation. Inadult tissues, aberrant Shh expression or signaling is implicated in thebiogenesis of multiple human cancers, including medulloblastoma, basalcell carcinoma, liver, pancreatic and urogenital tumors [See Pasca diMagliano, M., and Hebrok, M. (2003) Hedgehog signalling in cancerformation and maintenance, Nat Rev Cancer 3, 903-911.]

Hedgehog proteins undergo a unique set of post-translational processingreactions. Shh is synthesized as a 45 kDa precursor that trafficsthrough the secretory pathway. After the signal sequence is removed, Shhundergoes autocleavage to generate a 19 kDa N-terminal signalingmolecule, ShhN. During this reaction, cholesterol is attached to theC-terminus of ShhN. In addition, the N-terminal cysteine residue of ShhNis modified by palmitoylation. Unlike nearly all other knownpalmitoylated proteins, palmitate is attached via an amide bond to theN-terminus of ShhN. Palmitoylation of Hh and Shh is critical foreffective long- and short-range signaling. Mutation of the N-terminalCys to Ser or Ala results in a mutant protein with little or no activityin vivo or in vitro. Attachment of palmitate to Shh is catalyzed by themultipass membrane protein Hhat (Hedgehog acyltransferase). Hhat is amember of the membrane-bound O-acyl transferase (MBOAT) family. MostMBOAT family members catalyze transfer of long chain fatty acids tohydroxyl groups of lipids; however, Hhat is one of three MBOAT proteinsthat transfer fatty acids to protein substrates. In each case, fattyacid modification of the substrate protein is essential for itssignaling function.

The normal adult pancreas does not express Shh. However, aberrant Shhexpression can occur in the mature pancreas, where it plays a criticalrole in promoting pancreatic cancer [See Morton, J. P., and Lewis, B. C.(2007) “Shh signaling and pancreatic cancer: implications for therapy?”,Cell Cycle 6, 1553-1557.] Aberrant expression of Shh drivesproliferation of pancreatic cancer cells and formation of pancreaticintraepithelial neoplasms, and Hedgehog signaling is one of the corepathways altered in all human pancreatic cancers. Mouse models ofpancreatic cancer reveal that Shh functions synergistically withactivated K-Ras to promote and maintain tumorigenesis, while inhibitionof Shh signaling blocks pancreatic cancer invasion and metastasis [SeeOlive et al. (2009) “Inhibition of Hedgehog signaling enhances deliveryof chemotherapy in a mouse model of pancreatic cancer”, Science 324,1457-1461 and Feldmann et al. (2007) “Blockade of hedgehog signalinginhibits pancreatic cancer invasion and metastases: a new paradigm forcombination therapy in solid cancers”, Cancer Res. 67, 2187-2196.]

There is an urgent need for novel therapeutics to treat pancreaticcancer. We describe herein Hhat inhibitors that block Shhpalmitoylation, and thus provide opportunities for efficacious treatmentof pancreatic cancer.

SUMMARY OF THE INVENTION

The compounds of the invention are useful as anticancer agents,particularly in the treatment of Shh-driven cancers such as pancreaticcancer, gastric cancer, colon cancer, prostate cancer, osteosarcoma andsmall cell lung cancer.

In one aspect, the invention relates to a compound of formula I

wherein

-   R¹ and R² are independently selected from H, halogen,    (C₁-C₄)hydrocarbyl, (C₁-C₄)alkoxy, trifluoromethyl,    trifluoromethoxy, cyano and nitro;-   R³ is selected from (C₁-C₁₀)hydrocarbyl, (C₁-C₆)oxaalkyl and    heterocyclylalkyl; and-   R⁴ is selected from H, methyl, halomethyl, dihalomethyl, and    trihalomethyl.

In another aspect, the invention relates to a pharmaceutical compositioncomprising a pharmaceutically acceptable carrier and a compound offormula I.

In another aspect, the invention relates to a method for treating anShh-driven cancer comprising administering to a patient having such acancer a therapeutically effective amount of a compound of formula I.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts a graph of tumor volume versus time comparing cells inwhich Shh and Hhat have been suppressed with control cells.

FIG. 2 depicts a bar graph showing counts per minute of radiolabeledpalmitate residue incorporated into Shh peptide with controls and in thepresence and absence of compounds 13 and 14.

FIG. 3 depicts a bar graph showing cell counts of human pancreaticcancer cells in the presence and absence of compound 13.

DETAILED DESCRIPTION OF THE INVENTION

In a composition aspect, the invention relates to a compound of formulaI

as described above. In some embodiments, A is chosen from pyrrolidine,furan, thiophene and pyridine. In some embodiments, R¹ may be H and R²may be H or methyl. In other embodiments, A is phenyl. In theseembodiments, R¹ may be ortho relative to the point of attachment ofphenyl to the thieno[3,2-c]pyridine and R² may be para to the point ofattachment of phenyl to the thieno[3,2-c]pyridine. Such compounds wouldbe represented by formula II:

In some of these compounds, R¹ may be H or methyl and R² may be chosenfrom H, methyl, methoxy, chloro and fluoro. In others, R¹ and R² may bethe same and may be chosen from H and halogen.

In some embodiments, R³ may be selected from (C₁-C₁₀)alkyl,(C₁-C₆)oxaalkyl and heterocyclylalkyl. In some embodiments, R³ may bechosen from (C₃-C₆)alkyl, (C₃-C₆)alkenyl, (C₃-C₆)cycloalkyl,(C₁-C₆)oxaalkyl, furanyl(C₁-C₄)alkyl, thienyl(C₁-C₄)alkyl,pyrrolyl(C₁-C₄)alkyl, pyrrolidinyl(C₁-C₄)alkyl andtetrahydrofuranyl(C₁-C₄)alkyl. In particular examples, R³ ismethoxyethyl, methoxypropyl, ethoxypropyl, isopropyl, cyclopropyl, allylor furanylmethyl.

In some embodiments, R⁴ is hydrogen.

Throughout this specification the terms and substituents retain theirdefinitions.

Alkyl is intended to include linear or branched saturated hydrocarbonstructures. Examples of alkyl groups include methyl, ethyl, propyl,isopropyl, butyl, s-and t-butyl, 1-methyl-3-ethyloctyl and the like.Preferred alkyl groups are those of C₂₀ or below.

Cycloalkyl is for the purposes herein distinguished from alkyl andincludes cyclic hydrocarbon groups of from 3 to 10 carbon atoms.Examples of cycloalkyl groups include c-propyl, c-butyl, c-pentyl,norbornyl, decahydronaphthyl and the like.

Alkoxy or alkoxyl refers to groups of from 1 to 8 carbon atoms of astraight or branched configuration attached to the parent structurethrough an oxygen. Examples include methoxy, ethoxy, propoxy, isopropoxyand the like.

Aryl and heteroaryl generally refer to a 5- or 6-membered aromatic orheteroaromatic ring containing 0-3 heteroatoms selected from O, N, or S;a bicyclic 9- or 10-membered aromatic or heteroaromatic ring systemcontaining 0-3 heteroatoms selected from O, N, or S; or a tricyclic 13-or 14-membered aromatic or heteroaromatic ring system containing 0-3heteroatoms selected from O, N, or S. In the embodiments describedherein, the ring A is limited to 5- or 6-membered aromatic orheteroaromatic rings such as benzene, pyrrole, imidazole, pyridine,thiophene, thiazole, isothiazole, oxazole, isoxazole, furan, pyrimidine,pyrazine, tetrazole and pyrazole.

Arylalkyl means an aryl ring attached to an alkyl residue in which thepoint of attachment to the parent structure is through the alkyl.Examples are benzyl, phenethyl and the like. Heteroarylalkyl means analkyl residue attached to a heteroaryl ring. Examples include, e.g.,pyridinylmethyl, pyrimidinylethyl and the like.

C₁ to C₁₀ hydrocarbon (or, when describing a substituent, hydrocarbyl)means a linear, branched, or cyclic residue comprised of hydrogen andcarbon as the only elemental constituents. The term includes alkyl,cycloalkyl, polycycloalkyl, alkenyl, alkynyl, aryl and combinationsthereof. Examples include benzyl, phenethyl, cyclohexylmethyl,cyclopropylmethyl, cyclobutylmethyl, allyl, camphoryl and naphthylethyl.

Oxaalkyl refers to alkyl residues in which one or more carbons (andtheir associated hydrogens) have been replaced by oxygen. Examplesinclude methoxypropoxy, 3,6,9-trioxadecyl and the like. The termoxaalkyl is intended as it is understood in the art [see Naming andIndexing of Chemical Substances for Chemical Abstracts, published by theAmerican Chemical Society, 196, but without the restriction of 127(a)],i.e. it refers to compounds in which the oxygen is bonded via a singlebond to its adjacent atoms (forming ether bonds); it does not refer todoubly bonded oxygen, as would be found in carbonyl groups.

Unless otherwise specified, the term “carbocycle” is intended to includering systems in which the ring atoms are all carbon but of any oxidationstate. Thus (C₃-C₁₀) carbocycle refers to both non-aromatic and aromaticsystems, including such systems as cyclopropane, benzene andcyclohexene; (C₈-C₁₂) carbopolycycle refers to such systems asnorbornane, decalin, indane and naphthalene. Carbocycle, if nototherwise limited, refers to monocycles, bicycles and polycycles.

Heterocycle means a cycloalkyl or aryl residue in which one to two ofthe carbons is replaced by a heteroatom such as oxygen, nitrogen orsulfur. Heteroaryls form a subset of heterocycles. Examples ofheterocycles include pyrrolidine, pyrazole, pyrrole, imidazole, indole,quinoline, isoquinoline, tetrahydroisoquinoline, benzofuran,benzodioxan, benzodioxole (commonly referred to as methylenedioxyphenyl,when occurring as a substituent), tetrazole, morpholine, thiazole,pyridine, pyridazine, pyrimidine, pyrazine, thiophene, furan, oxazole,oxazoline, isoxazole, dioxane, tetrahydrofuran and the like.

As used herein, the term “optionally substituted” may be usedinterchangeably with “unsubstituted or substituted”. The term“substituted” refers to the replacement of one or more hydrogen atoms ina specified group with a specified radical. Substituted alkyl, aryl,cycloalkyl, heterocyclyl etc. refer to alkyl, aryl, cycloalkyl, orheterocyclyl wherein one or more H atoms in each residue are replacedwith halogen, haloalkyl, alkyl, acyl, alkoxyalkyl, hydroxyloweralkyl,hydroxy, loweralkoxy, haloalkoxy, oxaalkyl, carboxy, nitro, amino,alkylamino, and/or dialkylamino. In one embodiment, 1, 2 or 3 hydrogenatoms are replaced with a specified radical. In the case of alkyl andcycloalkyl, more than three hydrogen atoms can be replaced by fluorine;indeed, all available hydrogen atoms could be replaced by fluorine.

The compounds described herein may contain, in a substituent R^(x),double bonds and may also contain other centers of geometric asymmetry;unless specified otherwise, it is intended that the compounds includeboth E and Z geometric isomers. Likewise, all tautomeric forms are alsointended to be included. The compounds possess an asymmetric center atC-4 and may contain, in a substituent R^(x), additional asymmetriccenters and may thus give rise to enantiomers, diastereomers, and otherstereoisomeric forms that may be defined, in terms of absolutestereochemistry, as (R)— or (S)—. The present invention is meant toinclude all such possible isomers, as well as their racemic andoptically pure forms. Optically active (R)— and (S)— isomers may beprepared using chiral synthons or chiral reagents, or resolved usingconventional techniques.

As used herein, and as would be understood by the person of skill in theart, the recitation of “a compound”—unless expressly further limited—isintended to include salts of that compound. In a particular embodiment,the term “compound of formula I” refers to the compound or apharmaceutically acceptable salt thereof.

The term “pharmaceutically acceptable salt” refers to salts whosecounter ion (anion) derives from pharmaceutically acceptable non-toxicacids including inorganic acids and organic acids. Suitablepharmaceutically acceptable acids for salts of the compounds of thepresent invention include, for example, acetic, adipic, alginic,ascorbic, aspartic, benzenesulfonic (besylate), benzoic, boric, butyric,camphoric, camphorsulfonic, carbonic, citric, ethanedisulfonic,ethanesulfonic, ethylenediaminetetraacetic, formic, fumaric,glucoheptonic, gluconic, glutamic, hydrobromic, hydrochloric,hydroiodic, hydroxynaphthoic, isethionic, lactic, lactobionic,laurylsulfonic, maleic, malic, mandelic, methanesulfonic, mucic,naphthylenesulfonic, nitric, oleic, pamoic, pantothenic, phosphoric,pivalic, polygalacturonic, salicylic, stearic, succinic, sulfuric,tannic, tartaric acid, teoclatic, p-toluenesulfonic, and the like.

It will be recognized that the compounds of this invention can exist inradiolabeled form, i.e., the compounds may contain one or more atomscontaining an atomic mass or mass number different from the atomic massor mass number usually found in nature. Alternatively, a plurality ofmolecules of a single structure may include at least one atom thatoccurs in an isotopic ratio that is different from the isotopic ratiofound in nature. Radioisotopes of hydrogen, carbon, phosphorous,fluorine, chlorine and iodine include ²H, ³H, ¹¹C, ¹³C, ¹⁴C, ¹⁵N, ³⁵S,¹⁸F, ₃₆Cl, ¹²⁵I, ¹²⁴I and ¹³¹I respectively. Compounds that containthose radioisotopes and/or other radioisotopes of other atoms are withinthe scope of this invention. Tritiated, i.e. ³H, and carbon-14, i.e.,¹⁴C, radioisotopes are particularly preferred for their ease inpreparation and detectability. Compounds that contain isotopes ¹¹C, ¹³N,¹⁵O, ¹²⁴I and ¹⁸F are well suited for positron emission tomography.Radiolabeled compounds of formula I of this invention and prodrugsthereof can generally be prepared by methods well known to those skilledin the art. Conveniently, such radiolabeled compounds can be prepared bycarrying out the procedures disclosed in Schemes 1 and 2 by substitutinga readily available radiolabeled reagent for a non-radiolabeled reagent.

Although this invention is susceptible to embodiment in many differentforms, preferred embodiments of the invention are shown. It should beunderstood, however, that the present disclosure is to be considered asan exemplification of the principles of this invention and is notintended to limit the invention to the embodiments illustrated. In afirst aspect, the invention relates to compounds; in a second aspect theinvention relates to pharmaceutical compositions; in a third aspect, theinvention relates to methods. Both the second aspect of the inventionand the third aspect envision the use of any and all compounds of theformula I in the method of treatment. However, due to the peculiaritiesof patent law, and having nothing whatever to do with the scope of theinventors' conception of the invention, certain compounds appear from apreliminary search of the literature ineligible to be claimed ascompounds. Thus, for example, compounds in which R³ is cyclopropyl, R⁴is H and A is 4-t-butylphenyl, 4-methoxyphenyl, 4-methylphenyl,2-methylphenyl, 4-chlorophenyl, phenyl, 4-fluorophenyl or2,4-dichlorophenyl appear to be known. Similarly, compounds in which R³is cyclohexyl, R⁴ is H and A is 2-methylphenyl or 2,4-dichlorophenylappear to be known. In all of these cases, the compounds are disclosedin Chemical Abstracts only as members of a library, with no disclosedutility. Therefore, while these compounds are part of the inventiveconcept, they have been excluded from the claims to compounds, per se.It may be found upon further examination that certain members of theclaimed genus are not patentable to the inventors in this application.In this event, subsequent exclusions of species from the compass ofapplicants' claims are to be considered artifacts of patent prosecutionand not reflective of the inventors' concept or description of theirinvention; the invention encompasses all of the members of the genus Ithat are not already in the possession of the public.

While it may be possible for the compounds of formula I to beadministered as the raw chemical, it is preferable to present them as apharmaceutical composition. According to a further aspect, the presentinvention provides a pharmaceutical composition comprising a compound offormula I or a pharmaceutically acceptable salt or solvate thereof,together with one or more pharmaceutically carriers thereof andoptionally one or more other therapeutic ingredients. The carrier(s)must be “acceptable” in the sense of being compatible with the otheringredients of the formulation and not deleterious to the recipientthereof. The compositions may be formulated for oral, topical orparenteral administration. For example, they may be given intravenously,intraarterially, intraperitoneally, intratumorally or subcutaneously.

Formulations include those suitable for oral, parenteral (includingsubcutaneous, intradermal, intramuscular, intravenous andintraarticular), rectal and topical administration. The compounds arepreferably administered orally or by injection (intravenous,intramuscular, intraperitoneally, intratumorally or subcutaneous). Theprecise amount of compound administered to a patient will be theresponsibility of the attendant physician. However, the dose employedwill depend on a number of factors, including the age and sex of thepatient, the precise disorder being treated, and its severity. Also, theroute of administration may vary depending on the condition and itsseverity. The formulations may conveniently be presented in unit dosageform and may be prepared by any of the methods well known in the art ofpharmacy. In general, the formulations are prepared by uniformly andintimately bringing into association the active ingredient with liquidcarriers or finely divided solid carriers or both and then, ifnecessary, shaping the product into the desired formulation.

Formulations of the present invention suitable for oral administrationmay be presented as discrete units such as capsules, cachets or tabletseach containing a predetermined amount of the active ingredient; as apowder or granules; as a solution or a suspension in an aqueous liquidor a non-aqueous liquid; or as an oil-in-water liquid emulsion or awater-in-oil liquid emulsion. The active ingredient may also bepresented as a bolus, electuary or paste.

A tablet may be made by compression or molding, optionally with one ormore accessory ingredients. Compressed tablets may be prepared bycompressing in a suitable machine the active ingredient in afree-flowing form such as a powder or granules, optionally mixed with abinder, lubricant, inert diluent, lubricating, surface active ordispersing agent. Molded tablets may be made by molding in a suitablemachine a mixture of the powdered compound moistened with an inertliquid diluent. The tablets may optionally be coated or scored and maybe formulated so as to provide sustained, delayed or controlled releaseof the active ingredient therein.

Formulations for parenteral administration include aqueous andnon-aqueous sterile injection solutions which may contain anti-oxidants,buffers, bacteriostats and solutes which render the formulation isotonicwith the blood of the intended recipient. Formulations for parenteraladministration also include aqueous and non-aqueous sterile suspensions,which may include suspending agents and thickening agents. Theformulations may be presented in unit-dose or multi-dose containers, forexample sealed ampoules and vials, and may be stored in a freeze-dried(lyophilized) condition requiring only the addition of a sterile liquidcarrier, for example saline, phosphate-buffered saline (PBS) or thelike, immediately prior to use. Extemporaneous injection solutions andsuspensions may be prepared from sterile powders, granules and tabletsof the kind previously described.

Preferred unit dosage formulations are those containing an effectivedose, as herein below recited, or an appropriate fraction thereof, ofthe active ingredient.

It should be understood that in addition to the ingredients particularlymentioned above, the formulations of this invention may include otheragents conventional in the art having regard to the type of formulationin question, for example those suitable for oral administration mayinclude flavoring agents.

As used herein, “treatment” or “treating,” or “palliating” or“ameliorating” are used interchangeably herein. These terms refer to anapproach for obtaining beneficial or desired results including but notlimited to therapeutic benefit and/or a prophylactic benefit. Bytherapeutic benefit is meant eradication or amelioration of theunderlying disorder being treated. Also, a therapeutic benefit isachieved with the eradication or amelioration of one or more of thephysiological symptoms associated with the underlying disorder such thatan improvement is observed in the patient, notwithstanding that thepatient may still be afflicted with the underlying disorder. Forprophylactic benefit, the compositions may be administered to a patientreporting one or more of the physiological symptoms of a disease, eventhough a diagnosis of this disease may not have been made.

A comprehensive list of abbreviations utilized by organic chemists (i.e.persons of ordinary skill in the art) appears in the first issue of eachvolume of the Journal of Organic Chemistry. The list, which is typicallypresented in a table entitled “Standard List of Abbreviations” isincorporated herein by reference.

The compounds employed in the methods and pharmaceutical compositionsdescribed above are commercially available or may be synthesized byprocesses known in the art. In general, the synthesis may beschematically described as in Schemes 1 and 2. An aromatic aldehyde isreacted with an aminoethylthiophene under Pictet-Spengler conditions toprovide an 4-aryl-4,5,6,7-tetrahydrothieno[3,2-c]pyridine.Alternatively, an aromatic acid may be reacted with anaminoethylthiophene to provide the amide and the amide reacted underBischler-Napieralski conditions to provide the4-aryl-6,7-dihydrothieno[3,2-c]pyridine, which is reduced with aborohydride reagent to provide the4-aryl-4,5,6,7-tetrahydrothieno[3,2-c]pyridine. Both these routes aredescribed in Madsen et al. Bioorg. Med. Chem. 8, 2277-2289 (2000), whichis incorporated herein by reference.

The 4-aryl-4,5,6,7-tetrahydrothieno[3,2-c]pyridine may then be reactedwith an activated glycine derivative (the acyl component) by any of themany means well known in the art, particularly in the art of thesynthesis of peptides. Such agents include carbodiimides of varioussorts, mixed anhydrides, EEDQ, HATU, and the like. It is also possibleto pre-react the carboxylic acid with an appropriate leaving group toform an activated ester. Activated esters denote esters which arecapable of undergoing a substitution reaction with the secondary amineto form an amide. The term includes esters “activated” by neighboringelectron withdrawing substituents. Examples include esters of phenols,particularly electronegatively substituted phenol esters such aspentafluorophenol esters; O-esters of isourea, such as arise frominteraction with carbodiimides; O-esters of N-hydroxyimides andN-hydroxy heterocycles; specific examples include S-t-butyl esters,S-phenyl esters, S-2-pyridyl esters, N-hydroxypiperidine esters,N-hydroxysuccinimide esters, N-hydroxyphthalimide esters andN-hydroxybenzotriazole esters. The carboxyl may also be activated bypre-reaction to provide acyl halides, such as acid chlorides andfluorides.

During condensation, the activated glycine will usually be protectedwith one of the common protecting groups, R¹⁰, known in the peptide art.The protecting group, when present, will then be cleaved with a suitablecleaving agent to provide the 5-acyl-6,7-dihydrothieno[3,2-c]pyridinesof formula I. Protecting groups for the amine are discussed in standardtextbooks in the field of chemistry, such as Protective Groups inOrganic Synthesis by T. W. Greene and P. G. M. Wuts [John Wiley & Sons,New York, 1999], which is incorporated herein by reference. Particularattention is drawn to the chapter entitled “Protection for the AminoGroup” (pages 494-614). Common protecting groups include, t-Boc, Fmocand the like. Cleavage of t-Boc is accomplished by treatment with anacid, usually trifluoroacetic acid; cleavage of Fmoc is usuallyaccomplished by treatment with a nucleophile such as piperidine ortetrabutylammonium fluoride.

Fourteen examples of compounds of the genus I have been prepared andtested according to the protocol described below.

Radioiodination of iodo-palmitate with [¹²⁵I] NaI and synthesis of¹²⁵I-iodo-palmitoyl and 3H-palmitoyl CoA derivatives using CoAsynthetase were carried out as described by Berthiaume, L., et al.“Synthesis and use of iodo-fatty acid analogs”. Methods Enzymol. 250,454-466 (1995) and Peseckis, S. M., et al. (1993) “Iodinated fatty acidsas probes for myristate processing and function. Incorporation intopp60v-src”. J. Biol. Chem. 268, 5107-5114. The final concentrations ofpurified ¹²⁵I-iodo-palmitoyl CoA and ³H-palmitoyl CoA, were determinedfrom the absorbance at 260 nm using the extinction coefficient forpalmitoylCoA.

A cell based assay was used to monitor Shh palmitoylation. COS-1 cellsexpressing Shh, Fyn, or ShhGFP fusions and Hhat were starved for 1 hr inDMEM containing 2% dialysed fetal calf serum, followed by incubationwith 10-20 μCi/mL [¹²⁵I] IC16 or 4 hrs at 37 C. Cells were washed twicewith 2 ml of ice cold STE (100 mM NaCl, 10 mM Tris, 1 mM EDTA [pH 7.4])and lysed in 500 μl of RIPA Buffer (150 mM NaCl, 50 mM Tris, pH 7.4, 1%Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS, 1 mM EDTA). Lysateswere clarified by ultracentrifugation at 100,000×g for 15 min in aT100.2 rotor (Beckman, Fullerton, Calif.). Protein levels weredetermined by SDS-PAGE and Western blot analysis. Immunoprecipitationswere performed by incubating clarified lysates with 5 μl of theappropriate antibody and 50 μl of protein A/G+ agarose beads (Santa CruzBiotechnology) at 4° C. for 16 hrs. The beads were washed twice with 500μl of RIPA buffer. The final bead pellets were resuspended in 40 μl of2× SDS-PAGE sample buffer containing 40 mM DTT. Immunoprecipitatedsamples were run on a 12.5% SDS-PAGE gel, dried, and exposed byphosphorimaging for 2-3 days. Screens were analyzed on a FLA-7000phosphorimager (Fuji). Labelings were performed in duplicate andrepeated three times. For hydroxylamine treatment, gels were soaked ineither 1M Tris or hydroxylamine, pH 8.0 for 1 hr, then dried andanalyzed as above.

Expression and purification of recombinant Shh were carried out asdescribed in Buglino, J. A. and Resh, M. D. “Hhat is a palmitoylacyltransferase with specificity for N-palmitoylation of sonic hedgehog”. J.Biol. Chem. 283, 22076-22088 (2008) and Buglino, J. A. and Resh, M. D.“Identification of conserved regions and residues within Hedgehogacyltransferase critical for palmitoylation of Sonic Hedgehog”. PLoS One5, e11195 (2010). N-terminally 6× His tagged human Shh 24-197 with anenterokinase cleavage site immediately upstream of residue 24 wasamplified using full length Shh as a template. The purified PCR productwas ligated in NcoI and BamHI cut PET19b (Novagen). C24S and C24Aconstructs were generated by site directed mutagenesis using the QuickChange mutagenesis kit. All mutations were confirmed by sequencing.His-tagged Shh24-197 constructs were expressed in E. coli BL21(DE3)codon plus (Novagen), purified on Ni-NTA-agarose resin (Qiagen), anddialyzed (20 mM Tris-HCl, pH 8.0, 350 mM NaCl, 1 mM β-mercaptoethanol)in the presence of enterokinase (New England Biolabs). The dialyzedproduct was further purified by size exclusion chromatography on aSuperdex 75 column (GE Heathcare). Pooled fractions after size exclusionchromatography were concentrated to 3.0-3.5 mg/ml in 20 mM HEPES, pH7.3, 100 mM NaCl, 1 mM DTT. Protein concentration was measured using theDC protein assay (BioRad). The N-terminii of both wild type and mutantproteins were confirmed by Edman degradation.

HhatHAFlagHis was purified as follows. 20×100 mm plates of 293FT cellswere transfected with HhatHAFlagHis or pcDNA3.1 empty vector. 48 hrspost transfection, the cells were placed on ice, washed twice with 5 mlof ice cold STE, and then scraped into 5 ml of STE per plate. Cells werepelleted by centrifugation at 1000×G for 10 min. Cell pellets wereresuspended in 8 ml of cold hypotonic lysis buffer (0.2 mM MgCl2, 10 mMHEPES, pH 7.3). After 15 min incubation on ice, cells were lysed by 30up/down strokes in a Dounce homogenizer with a tight fitting pestle.After lysis, 2 ml of 1.25M sucrose was added to yield 10 ml of totalcell lysate. The lysate was separated into soluble (S100) and membrane(P100) fractions by ultracentrifugation at 100,000×G for 45 min in a Ti70.1 fixed angle rotor (Beckman). After centrifugation, the supernatantwas saved and the P100 pellets were resuspended in 10 ml of HypotonicLysis Buffer plus 0.25M sucrose and recentrifuged as above. Theresultant supernatant was combined with the supernatant from the firstspin for a total of 20 ml S100. The P100 membranes were againresuspended in 10 ml hypotonic lysis buffer +0.25M sucrose andrecentrifuged as above. The supernatant was discarded and the pelletswere resuspended in 10 ml of wash/solubilization buffer (20 mM HEPES, pH7.3, 350 mM NaCl, 1% octylglucoside, 1% glycerol) and incubated on icefor 1 hr, followed by centrifugation at 100,000×g. The resultant pelletwas discarded and the supernatant (detergent soluble fraction) wastransferred to a 15 ml tube and 500 ml of Flag M2 resin (Sigma) wasadded. Following a 1 hr incubation, the Flag resin was pelleted bycentrifugation at 1000×g and washed 4 times with 5 ml ofsolubilization/wash buffer. HhatHAFlagHis was eluted with 1.5 ml ofsolubilization/wash buffer supplemented with 300 ng/ml 3×FlagPeptide.The purified sample was concentrated and buffer exchanged to a finalvolume of 0.5-1.0 ml in 20 mM HEPES, pH 7.3, 100 mM NaCl, 1%octylglucoside, 1% glycerol. Protein concentrations were determinedusing the DC Protein Assay. The concentration of the final Flag eluatewas determined from the absorbance at 280 nm using an extinctioncoefficient of 193045 cm⁻¹M⁻¹. Samples of the final purified fractionwere subjected to SDS-PAGE and silver staining

In vitro palmitoylation was assayed according to Buglino, J. A. andResh, M. D. “Hhat is a palmitoylacyl transferase with specificity forN-palmitoylation of sonic hedgehog”. J. Biol. Chem. 283, 22076-22088(2008) The in vitro assay was performed by incubating 10 μL ofHhatHAFlagHis in 20 mM HEPES, pH 7.3, 100 mM NaCl, 1% octylglucoside, 1%glycerol with 10 μl of recombinant Shh (0.2-0.4 mg/mL in 20 mM MES, pH6.5, 1 mM EDTA, 1 mM DTT), followed by the addition of 30 μL of reactionbuffer (167 mM MES, pH 6.5, 1.7 mM DTT, 0.083% Triton X-100, 167 μM¹²⁵I-iodo-palmitate CoA). The reaction was stopped by the addition of504 of 2× sample buffer with 40 mM DTT. Samples were electrophoresed on12.5% SDS-PAGE gels, which were stained with Coomassie Blue, dried andexposed to phosphorimager for12-18hrs. After phosphorimaging, each Shhcontaining gel band was excised. ¹²⁵I-iodo-palmitate incorporation wasmeasured by counting in a Perkin-Elmer Gamma counter. Non-enzymaticincorporation of ¹²⁵I-iodo-palmitate into Shh was corrected for bysubtraction of counts from matched pcDNA 3.1 mock purification controls.

C-terminally biotinylated peptides corresponding to the first 10 aminoacids of Shh (CGPGRGFGKR), N-terminal acetylated Shh (Acetyl-CGPGRGFGKR)and C24A Shh (AGPGRGFGKR) were synthesized by the Sloan-KetteringMicrochemistry Core Facility. Purified peptides were palmitoylated invitro as outlined above except that the final Shh peptide concentrationwas 100 μM. After incubation, 400 μL of RIPA buffer and 50 μl ofStreptavidin-agarose beads were added, and the mixture was incubated for1 hr at 4° C. with continuous mixing. Biotinylated peptides werepelleted by centrifugation at 1000×g for 5 minutes. Pellets were washedtwice with 500 mL RIPA buffer. ¹²⁵I-iodo-palmitate incorporation wasdetermined by Gamma counting. Samples were incubated in either 1M Tris,pH 8.0, or hydroxylamine, pH 8.0 for 1 hr at room temperature followedby 2 washes in RIPA buffer.

To show knockdown of Shh and Hhat in human pancreatic cancer cells,shRNAs directed against human Shh or Hhat were cloned into the pLKO1vector. Human pancreatic cancer cell lines Panc1 and AsPC1 weretransfected and selected for 10-14 days in puromycin. Analyses of Shhand Hhat mRNA levels were performed by RT-qPCR. The results establishedthat knockdown of either Shh or Hhat inhibits both anchorage-dependentand anchorage-independent cell growth.

Xenograft experiments were performed under Animal Protocol #11-02-003.Panc-1 cells were transfected with pLKO.1 encoding shRNAs directedagainst Shh, Hhat, or a scrambled (Scr) control. pLKO.1 is alentivirus-based vector (Open Biosystems) that does not replicate, isself-inactivating, and is designed to deliver silencing shRNAs to tissueculture cells. Cells were grown in tissue culture for 10 days to allowfor knockdown of the designated gene. Aliquots of cells were analyzed byRT-qPCR analysis to verify that >80% knockdown of Shh or Hhat had beenachieved. A separate culture of Panc-1 cells that were not treated(Untr) with pLKO.1 were maintained as a control for any effect of pLKO.1on tumor growth. Fifteen million Panc-1 cells were injected into theflanks of athymic (nude) female mice. Tumor measurements were taken witha caliper twice a week and plotted. The results are shown in FIG. 1. Atthe end of 71 days, tumor mass in the Shh or Hhat-depleted cells wasless than 30% of control, showing that inhibition of Shh or Hhatcorrelates with tumor suppression.

Hhat activity assay: Five μl of 10 mM MES, pH 6.5 buffer was dispensedwithin each well of a 384-well white/clear-bottom plate (GreinerBio-One, Kremsmuenster, Austria) using a Thermo Multi-Drop Combidispenser. Compounds (12.5 μM final concentration) were dispensed usinga Janus “Varispan” automated syringe pipette. Next, 34 of P100 membranesfrom HA-Hhat transfected 293FT cells were dispensed with the ThermoMulti-Drop Combi dispenser, and incubated for 20 min at roomtemperature. The reaction was started by the addition of 12 μL ofreaction buffer (167 mM MES, pH 6.5, 2 mM DTT, 0.083% Triton X-100, 8.3μM 125-I-iodo-palmitoylCoA, 5.21 μM Shh biotinylated peptide). Followinga 1 hour incubation at room temperature, the reaction was stopped by theaddition of 70 μL SPA beads solution (7.14 mg/mL in RIPA buffer), andthe signal was detected on a Microbeta Trilux reader. Each plateincluded high control (DMSO only) and low control (0.125% TFA finalconcentration) rows. Percent inhibition for each experimental point wasdetermined by the formula: [(high control−compound)/(high control−lowcontrol)]*100.

Human pancreatic adenocarcinoma cell assay: 5000 AsPC1 (human pancreaticadenocarcinoma) cells were plated in each well of a 384-wellblack/clear-bottom tissue culture plate (Greiner Bio-One, Kremsmuenster,Austria), using Thermo Multi-Drop Combi dispenser. The plates wereincubated at 37° C. for 24 h before compounds were dispensed using aJanus “Varispan” automated syringe pipette at 50 μM final concentration.High control (DMSO only) and low control (cell media only) rows wereincluded in each plate. After 48 h incubation, Alamar Blue (Invitrogen)was added to each well in 1:100 ratio. 4 h later, cell viability wasassessed by measuring fluorescence on a Perkin-Elmer EnVision platereader.

Compounds tested and found effective were:

% In- hibi- Ex- tion am- of ple Hhat num- RU at 12.5 ber numberStructure μM  1 RU- 0072298

100.8  2 RU- 0072503

 98.9  3 RU- 0072407

 97.8  4 RU- 0072417

 96.2  5 RU- 0072436

 95.6  6 RU- 0072279

 94.7  7 RU- 0072513

 94.3  8 RU- 0072523

 94.3  9 RU- 0072130

 92.8 10 RU- 0072467

 91.6 11 RU- 0072268

 87.2 12 RU- 0072288

 17.1 13 RU-SKI 101

14 RU-SKI 201

Each of compounds 13 and 14 (20 μM) was incubated with purified Hhat inthe presence of saturating concentrations of ¹²⁵I-Iodopalmitoyl CoA+Shhpeptide as described above. Radiolabeled peptides were pulled down withstreptavidin agarose and the cpm incorporated into the peptide wasquantified in a gamma counter. As shown in FIG. 2, compounds 13 and 14are good inhibitors of Hhat activity, showing greater than 75% reductionin cpm.

Compound 13 was tested in the human pancreatic adenocarcinoma cellassay. The results are shown graphically in FIG. 3. At 10 μM it reducedthe proliferation of human pancreatic cancer cells 50% at day six. At 20μM it reduced the proliferation of human pancreatic cancer cells by 70%at day six.

IC50 values were generated for compound 13 (RU-SKI 101) and compound 14(RU-SKI 201) in an in vitro Hhat activity assay at saturating substrateconcentrations, using purified enzyme, 0.7 μM ShhN recombinant proteinand 18 μM ¹²⁵I-iodo-palmitoylCoA. The samples were incubated andincorporation into ShhN protein was quantified. Each experiment wasrepeated twice. The IC50 value for compound 13 was 2.05 μM and forcompound 14 was 0.68 μM.

1. A compound of formula

wherein R¹ and R² are independently selected from H, halogen,(C₁-C₄)hydrocarbyl, (C₁-C₄)alkoxy, trifluoromethyl, trifluoromethoxy,cyano and nitro; R³ is selected from (C₁-C₁₀)hydrocarbyl,(C₁-C₆)oxaalkyl and heterocyclylalkyl; R⁴ is selected from H, methyl,halomethyl, dihalomethyl, and trihalomethyl; and A is phenyl or a 5- or6-membered aromatic heterocycle; with the provisos that, (a) when R³ iscyclopropyl, R⁴ is H and A is phenyl, then the combination of R¹, R² andA cannot result in 4-t-butylphenyl, 4-methoxyphenyl, 4-methylphenyl,2-methylphenyl, 4-chlorophenyl, phenyl, 4-fluorophenyl or2,4-dichlorophenyl; and (b) when R³ is cyclohexyl, R⁴ is H and A isphenyl, then the combination of R¹, R² and A cannot result in2-methylphenyl or 2,4-dichlorophenyl.
 2. A pharmaceutical compositioncomprising a pharmaceutically acceptable carrier and a compound offormula

wherein R¹ and R² are independently selected from H, halogen,(C₁-C₄)hydrocarbyl, (C₁-C₄)alkoxy, trifluoromethyl, trifluoromethoxy,cyano and nitro; R³ is selected from (C₁-C₁₀)hydrocarbyl,(C₁-C₆)oxaalkyl and heterocyclylalkyl; R⁴ is selected from H, methyl,halomethyl, dihalomethyl, and trihalomethyl; and A is phenyl or a 5- or6-membered aromatic heterocycle.
 3. A compound or composition accordingto claim 1 wherein A is chosen from pyrrolidine, furan, thiophene andpyridine.
 4. A compound or composition according to claim 3 wherein R¹is H and R² is H or methyl.
 5. A compound or composition according toclaim 4 wherein A is pyridine.
 6. A compound or composition according toclaim 1 wherein A is phenyl.
 7. A compound or composition according toclaim 6 wherein R¹ is ortho relative to the point of attachment ofphenyl to the thieno[3,2-c]pyridine and R² is para to the point ofattachment of phenyl to the thieno[3,2-c]pyridine.
 8. A compound orcomposition according to claim 7 wherein R¹ is H or methyl and R² ischosen from H, methyl, methoxy, chloro and fluoro.
 9. A compound orcomposition according to claim 7 wherein R¹ and R² are the same and arechosen from H and halogen.
 10. A compound or composition according toclaim 1 wherein R³ is selected from (C₁-C₁₀)alkyl, (C₁-C₆)oxaalkyl andheterocyclylalkyl.
 11. A compound or composition according to claim 1wherein R³ is chosen from (C₃-C₆)alkyl, (C₃-C₆)alkenyl,(C₃-C₆)cycloalkyl, (C₁-C₆)oxaalkyl, furanyl(C₁-C₄)alkyl,thienyl(C₁-C₄)alkyl, pyrrolyl(C₁-C₄)alkyl, pyrrolidinyl(C₁-C₄)alkyl andtetrahydrofuranyl(C₁-C₄)alkyl.
 12. A compound or composition accordingto claim 11 wherein R³ is chosen from (C₃-C₆)alkyl, methoxyethyl,methoxypropyl, ethoxypropyl, isopropyl, cyclopropyl, allyl andfuranylmethyl.
 13. A compound or composition according to claim 1wherein R⁴ is hydrogen.
 14. A compound or composition according to claim1 wherein R¹ is meta relative to the point of attachment of phenyl tothe thieno[3,2-c]pyridine.
 15. A compound or composition according toclaim 14 wherein R¹ is methyl and R² is hydrogen.
 16. A method fortreating a patient having an Shh-driven cancer comprising administeringto said patient a therapeutically effective amount of a compound offormula

wherein R¹ and R² are independently selected from H, halogen,(C₁-C₄)hydrocarbyl, (C₁-C₄)alkoxy, trifluoromethyl, trifluoromethoxy,cyano and nitro; R³ is selected from (C₁-C₁₀)hydrocarbyl,(C₁-C₆)oxaalkyl and heterocyclylalkyl; R⁴ is selected from H, methyl,halomethyl, dihalomethyl, and trihalomethyl; and A is phenyl or a 5- or6-membered aromatic heterocycle.
 17. A method according to claim 16wherein said cancer is chosen from pancreatic cancer, gastric cancer,colon cancer, prostate cancer, osteosarcoma and small cell lung cancer.18. Use of a compound or composition according to claim 1 for themanufacture of a medicament for the treatment of an Shh-driven cancer.19. Use according to claim 18 wherein said cancer is chosen frompancreatic cancer, gastric cancer, colon cancer, prostate cancer,osteosarcoma and small cell lung cancer.